{
    "info": {
        "author": "Paul Blischak & Laura Kubatko",
        "author_email": "blischak.4@osu.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Programming Language :: Cython",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6"
        ],
        "description": "|Build Status| |Documentation|  |PyPI Badge|\n\nHyDe: hybridization detection using phylogenetic invariants\n-----------------------------------------------------------\n\n**Publication:**\n\nBlischak, P. D., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2018.\nHyDe: a Python package for genome-scale hybridization detection.\n*Systematic Biology*, doi: `https://doi.org/10.1093/sysbio/syy023 <https://doi.org/10.1093/sysbio/syy023>`__.\n\n`Read the Docs <http://hybridization-detection.rtfd.io/>`__\n-----------------------------------------------------------\n\nHyDe is a software package that detects hybridization in phylogenomic\ndata sets using phylogenetic invariants. The primary interface for HyDe is a Python\nmodule called ``phyde`` (**P**\\ ythonic **Hy**\\ bridization **De**\\ tection).\n``phyde`` provides a suite of tools for performing hypothesis tests on triples of taxa\nto detect hybridization. To ensure that the necessary\ndependencies for ``phyde`` are available, we suggest using a Python distribution such\nas `Miniconda <https://conda.io/miniconda.html>`__.\n\nTo facilitate analyses using the Python module, three scripts are provided to\nconduct hybridization detection analyses directly from the command line:\n\n- ``run_hyde.py``: runs a standard hybridization detection analysis on all triples\n  in all directions. Results are also filtered based on whether there is significant\n  evidence for hybridization.\n- ``individual_hyde.py``: tests each individual within a putative hybrid population\n  using a list of specified triples specified.\n- ``bootstrap_hyde.py``: conducts bootstrap resampling of the individuals within\n  the putative hybrid lineages for each specified triple.\n\nThese last two scripts need to be given a three column table of triples\n(P1, Hybrid, P2) that you wish to test:\n\n.. code::\n\n  sp1 sp2 sp3\n  sp1 sp3 sp4\n  sp3 sp4 sp5\n  .\n  .\n  .\n\nYou can also use a results file from a previous analysis as a triples file.\nFor example, you can use the filtered results from the ``run_hyde.py`` script so that\nyou only run analyses on triples that have significant levels of hybridization.\nIf you only have a few hypotheses that you want to test, then you can also pass\na triples file to ``run_hyde.py`` and it will only test those hypotheses rather than\ntesting everything.\n\nMultithreaded versions of these scripts are also available (``run_hyde_mp.py``,\n``individual_hyde_mp.py``, and ``bootstrap_hyde_mp.py``).\nMake sure you have the ``multiprocess`` module installed before you use them.\n\nGetting help\n------------\n\nIf you have questions about running HyDe, please feel free to use the\n**gitter chatroom** to get help:\n\n|Gitter|\n\nIf you have a problem while running HyDe and you think it may be a bug,\nplease consider filing an issue:\n\n|HyDe Issues|\n\nInstallation\n------------\n\nRequirements:\n~~~~~~~~~~~~~\n\n-  Python 2.7 or 3.6\n-  Python Modules:\n\n   -  Cython\n   -  Numpy\n   -  Matplotlib\n   -  Seaborn\n   -  Multiprocess\n\n-  C++ compiler\n\n.. code:: bash\n\n    # To install dependencies\n    pip install cython numpy matplotlib seaborn multiprocess\n\n    # Clone HyDe repository from GitHub\n    git clone https://github.com/pblischak/HyDe.git\n    cd HyDe\n\n    # Now install phyde module\n    python setup.py install\n\n    # Test the installation\n    make test\n\n    # Test multithreaded scripts\n    make test_threads\n\nThe ``phyde`` module is also hosted on the Python Package Index (PyPI), and can be installed directly using\n``pip``.\n\n.. code:: bash\n\n  # Install from PyPI with pip\n  pip install phyde\n\nDocumentation for analyzing data using HyDe can be found `here <http://hybridization-detection.readthedocs.io/analyze.html>`_.\n\n.. |Build Status| image:: https://travis-ci.org/pblischak/HyDe.svg?branch=master\n   :target: https://travis-ci.org/pblischak/HyDe\n\n.. |Documentation| image:: http://readthedocs.org/projects/hybridization-detection/badge/?version=latest\n   :target: http://hybridization-detection.readthedocs.io\n\n.. |PyPI Badge| image:: https://img.shields.io/pypi/v/phyde.svg\n   :target: https://pypi.python.org/pypi/phyde\n\n.. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg\n   :target: https://gitter.im/pblischak-HyDe/Lobby\n\n.. |HyDe Issues| image:: https://img.shields.io/badge/HyDe-Issues-blue.svg\n   :target: https://github.com/pblischak/HyDe/issues",
        "description_content_type": "",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/pblischak/HyDe",
        "keywords": "",
        "license": "GPLv3",
        "maintainer": "",
        "maintainer_email": "",
        "name": "phyde",
        "package_url": "https://pypi.org/project/phyde/",
        "platform": "",
        "project_url": "https://pypi.org/project/phyde/",
        "project_urls": {
            "Homepage": "https://github.com/pblischak/HyDe"
        },
        "release_url": "https://pypi.org/project/phyde/0.4.3/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "Hybridization detection using phylogenetic invariants",
        "version": "0.4.3"
    },
    "last_serial": 5478576,
    "releases": {
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "37f35b36f37d73f9593bbb7e4b5b2243",
                    "sha256": "9a3684208129f532d6255a07a86413d962efd73c90504aad92320a007ac641c3"
                },
                "downloads": -1,
                "filename": "phyde-0.1.0-cp27-cp27m-macosx_10_7_x86_64.whl",
                "has_sig": false,
                "md5_digest": "37f35b36f37d73f9593bbb7e4b5b2243",
                "packagetype": "bdist_wheel",
                "python_version": "cp27",
                "requires_python": null,
                "size": 388945,
                "upload_time": "2017-06-15T20:54:12",
                "url": "https://files.pythonhosted.org/packages/6a/eb/9aab39a62aefa1b08233c2d08aeea85b56b9304ba5bfef5976fd7f46bc08/phyde-0.1.0-cp27-cp27m-macosx_10_7_x86_64.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "53a8e384feb75c64de448e4677474bd7",
                    "sha256": "b90fcd92fa4dbcf17a80f166ce7694d0bd28d60381e17a284f04c427911212b5"
                },
                "downloads": -1,
                "filename": "phyde-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "53a8e384feb75c64de448e4677474bd7",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 206927,
                "upload_time": "2017-06-15T20:54:17",
                "url": "https://files.pythonhosted.org/packages/df/88/a54e12f2d3a41f9ece279f2b04c277edeba1b7c83c2cfb06b36f75cad906/phyde-0.1.0.tar.gz"
            }
        ],
        "0.1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "528f3d0fe0cd9ea5c010d32dbbcf34c3",
                    "sha256": "4e2fdd77dd8fa7091ff927a37128bff013c5602990440bde43387ed6ca922614"
                },
                "downloads": -1,
                "filename": "phyde-0.1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "528f3d0fe0cd9ea5c010d32dbbcf34c3",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 473920,
                "upload_time": "2017-06-16T15:04:39",
                "url": "https://files.pythonhosted.org/packages/78/b6/8220ecf88bf8a38ca3fbef374409fc9e22ef7e100c65c9ad2cdca4ec24f1/phyde-0.1.1.tar.gz"
            }
        ],
        "0.2.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "8030d1fd338016628635d640376615fb",
                    "sha256": "b69bf5885fd52243b8f9950dfcfc63f5473081c7cac61320f59f75e3ad478705"
                },
                "downloads": -1,
                "filename": "phyde-0.2.0.tar.gz",
                "has_sig": false,
                "md5_digest": "8030d1fd338016628635d640376615fb",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 473116,
                "upload_time": "2017-06-25T22:38:07",
                "url": "https://files.pythonhosted.org/packages/00/8d/218dd2aef71299c3b6ceccaa2e806947a57f2d354761f2311b5a5f50fb7c/phyde-0.2.0.tar.gz"
            }
        ],
        "0.2.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "9e1e17fd5bc98ecf7df42f8dded00747",
                    "sha256": "addeac02c11ff4f6bfbe93d034551215ffbcbebe17fc72d2982c6c75833ad007"
                },
                "downloads": -1,
                "filename": "phyde-0.2.3.tar.gz",
                "has_sig": false,
                "md5_digest": "9e1e17fd5bc98ecf7df42f8dded00747",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 427265,
                "upload_time": "2017-08-13T16:41:27",
                "url": "https://files.pythonhosted.org/packages/35/f0/8155278702de126cd0ac5b3f721969c25140fe90485b6f00fa7b258e9c26/phyde-0.2.3.tar.gz"
            }
        ],
        "0.3.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "d83cd8ed7a2fda68203149356603e824",
                    "sha256": "cf28c01cb590abbe8159c7f7f794ee81a4e1bf418104e9f680fafdfd16098e13"
                },
                "downloads": -1,
                "filename": "phyde-0.3.1.tar.gz",
                "has_sig": false,
                "md5_digest": "d83cd8ed7a2fda68203149356603e824",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 424649,
                "upload_time": "2017-09-18T16:36:10",
                "url": "https://files.pythonhosted.org/packages/ad/91/2a6452689eaa909c817dabac28f846da0483d96550bc60e46d6216b3edeb/phyde-0.3.1.tar.gz"
            }
        ],
        "0.3.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c3837372a53fb2d41118f79eb59dd000",
                    "sha256": "83bae73906205e219a528c523ec6a168fb7dc9cc0116a8e6c97e1ba32a7c9f9d"
                },
                "downloads": -1,
                "filename": "phyde-0.3.2.tar.gz",
                "has_sig": false,
                "md5_digest": "c3837372a53fb2d41118f79eb59dd000",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 428707,
                "upload_time": "2017-12-05T21:05:47",
                "url": "https://files.pythonhosted.org/packages/00/c8/85badf3d258d5a504acc76601fac9f00b6cbbecfc0673e061f847ed38502/phyde-0.3.2.tar.gz"
            }
        ],
        "0.3.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "4229d0b8ee185e0b50ec2093a18ff063",
                    "sha256": "74eed4298e54b60c9c732911bf9b3cdd47a11ed4d436c45a44310cc3a6499e4c"
                },
                "downloads": -1,
                "filename": "phyde-0.3.3.tar.gz",
                "has_sig": false,
                "md5_digest": "4229d0b8ee185e0b50ec2093a18ff063",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 430992,
                "upload_time": "2017-12-14T21:12:29",
                "url": "https://files.pythonhosted.org/packages/b6/d3/158c2ea2e49df353a5ad8af41faef826ac27c1ebdb73b69474137ca59e80/phyde-0.3.3.tar.gz"
            }
        ],
        "0.4.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "40d175a5a5b8e56e340943eb538c71cf",
                    "sha256": "f7ed67c8a77dd40f8009fb87334f35dcc68fdf5524b8121223cbaef3798667b3"
                },
                "downloads": -1,
                "filename": "phyde-0.4.0.tar.gz",
                "has_sig": false,
                "md5_digest": "40d175a5a5b8e56e340943eb538c71cf",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 639398,
                "upload_time": "2017-12-19T21:50:06",
                "url": "https://files.pythonhosted.org/packages/3c/b3/afb797906934f51b3f9d7dcb91b675eaaf4e32906e804252944658446eea/phyde-0.4.0.tar.gz"
            }
        ],
        "0.4.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "e659d29e9643e88177856ad6ec6d7319",
                    "sha256": "ed154721202f3a13022979fd90d08a6a88f41fd170bbf4c8bc526ec032fcf761"
                },
                "downloads": -1,
                "filename": "phyde-0.4.1.tar.gz",
                "has_sig": false,
                "md5_digest": "e659d29e9643e88177856ad6ec6d7319",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 638802,
                "upload_time": "2018-01-26T23:00:23",
                "url": "https://files.pythonhosted.org/packages/c5/3e/0135ef01a012dfe7a31012b4548a4a58fad5207af4818f22cea99ef3f9df/phyde-0.4.1.tar.gz"
            }
        ],
        "0.4.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c388e2d4ecec5f255ecaea4992896a4e",
                    "sha256": "27c7b005cfbebd329ac880332eb06ad4510521e6ef9a21414c35766d16c32ad1"
                },
                "downloads": -1,
                "filename": "phyde-0.4.2.tar.gz",
                "has_sig": false,
                "md5_digest": "c388e2d4ecec5f255ecaea4992896a4e",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 659457,
                "upload_time": "2018-03-17T09:35:21",
                "url": "https://files.pythonhosted.org/packages/fc/20/4d9bc5157ad9f099db673f752d32191005a01429a0eab831d7d09a41e533/phyde-0.4.2.tar.gz"
            }
        ],
        "0.4.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "54608d5b579a0ea1d6a895531c07d6ae",
                    "sha256": "4869acf3f05e68d92a0adaa095d1fc02036fa691596f4c02543249ccd00c469c"
                },
                "downloads": -1,
                "filename": "phyde-0.4.3.tar.gz",
                "has_sig": false,
                "md5_digest": "54608d5b579a0ea1d6a895531c07d6ae",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 668466,
                "upload_time": "2019-07-02T21:57:02",
                "url": "https://files.pythonhosted.org/packages/bd/9f/f3838df33ae03a331483ec6193e25d34a06b33d11d96313ac0fe6960e272/phyde-0.4.3.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "54608d5b579a0ea1d6a895531c07d6ae",
                "sha256": "4869acf3f05e68d92a0adaa095d1fc02036fa691596f4c02543249ccd00c469c"
            },
            "downloads": -1,
            "filename": "phyde-0.4.3.tar.gz",
            "has_sig": false,
            "md5_digest": "54608d5b579a0ea1d6a895531c07d6ae",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 668466,
            "upload_time": "2019-07-02T21:57:02",
            "url": "https://files.pythonhosted.org/packages/bd/9f/f3838df33ae03a331483ec6193e25d34a06b33d11d96313ac0fe6960e272/phyde-0.4.3.tar.gz"
        }
    ]
}